Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Where should metadata live? #58

Open
khoroshevskyi opened this issue Apr 9, 2024 · 1 comment
Open

Where should metadata live? #58

khoroshevskyi opened this issue Apr 9, 2024 · 1 comment
Labels
brainstorming enhancement New feature or request

Comments

@khoroshevskyi
Copy link
Member

As for this moment we have 2 types of metadata:

  1. user provided metadata ( stored in pephub)
  2. metadata generated by bedboss (stored in the db)

There are some important information in user provided metadata:

  • tissue type
  • organism id (9606)
  • organim name (Homo sapiens)
  • global experiment id (geo:gse123454)
  • global sample id (geo:gsm1234543)

WHERE does this information should live? This is important information and almost always is provided by user.
@khoroshevskyi khoroshevskyi added enhancement New feature or request brainstorming labels Apr 9, 2024
@khoroshevskyi
Copy link
Member Author

After discussion, we can standardize metadata by using bedmess, and add this metadata to sql database

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
brainstorming enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@khoroshevskyi